drake_md_report


HYPOTHESES

We selected only peaks seen in >1 of the 4 replicates (i.e. n = 2 or 3 or 4)


setup

how many FTICR reps per treatment type?

so we select formulae seen in at least 2 reps per treatment type


van krevelens

domains, baseline

fticr domains

VK by replication

VK by replication

VK by treatment

VK diagrams by treatment

VK unique

VK unique

unique to each amendment, in each incubation type


relative abundances

STATS

PERMANOVA

PCA

overall PCA

PCA individual treatments

individual cores


Session Info

click to expand

Date run: 2020-08-10

#> R version 4.0.2 (2020-06-22)
#> Platform: x86_64-apple-darwin17.0 (64-bit)
#> Running under: macOS Catalina 10.15.6
#> 
#> Matrix products: default
#> BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
#> 
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#>  [1] visNetwork_2.0.9 vegan_2.5-6      lattice_0.20-41  permute_0.9-5    rmarkdown_2.3    drake_7.12.4     ggbiplot_0.55   
#>  [8] PNWColors_0.1.0  forcats_0.5.0    stringr_1.4.0    dplyr_1.0.1      purrr_0.3.4      readr_1.3.1      tidyr_1.1.1     
#> [15] tibble_3.0.3     ggplot2_3.3.2    tidyverse_1.3.0  here_0.1        
#> 
#> loaded via a namespace (and not attached):
#>  [1] Rcpp_1.0.5        lubridate_1.7.9   txtq_0.2.3        prettyunits_1.1.1 assertthat_0.2.1  rprojroot_1.3-2   digest_0.6.25    
#>  [8] R6_2.4.1          cellranger_1.1.0  plyr_1.8.6        backports_1.1.8   reprex_0.3.0      evaluate_0.14     httr_1.4.2       
#> [15] pillar_1.4.6      rlang_0.4.7       progress_1.2.2    readxl_1.3.1      rstudioapi_0.11   blob_1.2.1        Matrix_1.2-18    
#> [22] labeling_0.3      splines_4.0.2     htmlwidgets_1.5.1 igraph_1.2.5      munsell_0.5.0     broom_0.7.0       compiler_4.0.2   
#> [29] modelr_0.1.8      xfun_0.16         pkgconfig_2.0.3   mgcv_1.8-31       htmltools_0.5.0   tidyselect_1.1.0  fansi_0.4.1      
#> [36] crayon_1.3.4      dbplyr_1.4.4      withr_2.2.0       MASS_7.3-51.6     grid_4.0.2        nlme_3.1-148      jsonlite_1.7.0   
#> [43] gtable_0.3.0      lifecycle_0.2.0   DBI_1.1.0         magrittr_1.5      storr_1.2.1       scales_1.1.1      cli_2.0.2        
#> [50] stringi_1.4.6     farver_2.0.3      fs_1.5.0          xml2_1.3.2        ellipsis_0.3.1    filelock_1.0.2    generics_0.0.2   
#> [57] vctrs_0.3.2       tools_4.0.2       glue_1.4.1        hms_0.5.3         yaml_2.2.1        parallel_4.0.2    colorspace_1.4-1 
#> [64] cluster_2.1.0     base64url_1.4     rvest_0.3.6       knitr_1.29        haven_2.3.1